clustalw-mpi

MPI-distributed global sequence alignment with ClustalW

ClustalW is a popular tool for multiple sequence alignment. The
alignment is achieved via three steps: pairwise alignment,
guide-tree generation and progressive alignment. ClustalW-MPI is an
MPI implementation of ClustalW. Based on
version 1.82 of the original ClustalW, both the pairwise
and progressive alignments are parallelized with MPI, a
popular message passing programming standard. The
pairwise alignments can be easily parallelized since the many
alignments are time independent on each other. However
the progressive alignments are essentially not parallelizable
because of the time dependencies between each alignment.

Here the recursive parallelism paradigm is applied to the linear space
profile-profile alignment algorithm. This approach is more time
efficient on computers with distributed memory architecture.
Traditional approach that relies on precomputing the profile-profile
score matrix has also been implemented. Results shown the latter is indeed
more appropriate for shared memory multiprocessor computer.

ClustalX is suggested for its support for local realignments, seaview
is a versatile editor of alignments.